US10174303B2 - Genetically engineered microorganisms for the production of chorismate-derived products - Google Patents

Genetically engineered microorganisms for the production of chorismate-derived products Download PDF

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US10174303B2
US10174303B2 US15/166,224 US201615166224A US10174303B2 US 10174303 B2 US10174303 B2 US 10174303B2 US 201615166224 A US201615166224 A US 201615166224A US 10174303 B2 US10174303 B2 US 10174303B2
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bacterium
chorismate
microorganism
synthase
clostridium
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US20160348087A1 (en
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James Bruce Yarnton Haycock Behrendorff
Michael Koepke
Loan Phuong Tran
Wyatt Eric Allen
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Lanzatech NZ Inc
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    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/10—Biofuels, e.g. bio-diesel

Definitions

  • the present invention relates to genetically engineered microorganisms and methods for the production of chorismate-derived products by microbial fermentation, particularly by microbial fermentation of a gaseous substrate.
  • catalytic processes may be used to convert gases containing carbon monoxide (CO) and/or carbon dioxide (CO 2 ) and hydrogen (H 2 ) into a variety of fuels and chemicals.
  • microorganisms may also be used to biologically convert such gases into fuels and chemicals.
  • Biological processes have several advantages over catalytic processes, including higher specificity, higher yields, lower energy costs, and greater catalyst resistance to poisoning.
  • CO is a major free energy-rich byproduct of the incomplete combustion of organic materials such as coal or oil and oil-derived products.
  • organic materials such as coal or oil and oil-derived products.
  • the steel industry in Australia is reported to produce and release into the atmosphere over 500,000 tonnes of CO annually.
  • microorganisms to grow on CO as a sole carbon source was first discovered in 1903. This was later determined to be a property of microorganisms that use the acetyl coenzyme A (acetyl-CoA) biochemical pathway of autotrophic growth, also known as the Wood-Ljungdahl pathway.
  • acetyl-CoA acetyl coenzyme A
  • Wood-Ljungdahl pathway also known as the Wood-Ljungdahl pathway.
  • a large number of anaerobic microorganisms including carboxydotrophic, photosynthetic, methanogenic, and acetogenic microorganisms have been shown to metabolize CO to various end products, namely CO 2 , H 2 , methane, n-butanol, acetate, and ethanol.
  • the aromatic compound para-hydroxybenzoic acid is a major monomer used in liquid crystal polymers and also used as a precursor for the production of parahydroxybenzoates or parahydroxybenzoic esters, commonly referred to as parabens.
  • Liquid crystal polymers include Kevlar and Vectran, which have multiple uses.
  • Parabens and their salts are used in a range of industries including the cosmetic, pharmaceutical and food industries. They are effective preservatives and can be used for their bactericidal and fungicidal properties in cosmetic and food formulations.
  • the invention provides a genetically engineered microorganism capable of producing chorismate-derived products.
  • the invention provides a genetically engineered microorganism capable of producing at least one chorismate-derived product, wherein the bacterium comprises at least one of (a) an exogenous chorismate pyruvate lyase (EC 4.1.3.40), (b) an exogenous isochorismate synthase (EC 5.4.4.2), (c) an exogenous isochorismate pyruvate lyase (EC 4.2.99.21), and (d) a prephenate synthase (EC 5.4.99.5) comprising a disruptive mutation.
  • the bacterium comprises at least one of (a) an exogenous chorismate pyruvate lyase (EC 4.1.3.40), (b) an exogenous isochorismate synthase (EC 5.4.4.2), (c) an exogenous isochorismate pyruvate lya
  • the genetically engineered microorganism is a C1-fixing bacterium, such as a Clostridium bacterium, capable of producing at least one chorismate-derived product by fermentation of a C1-containing gaseous substrate.
  • the chorismate pyruvate lyase may be ubiC
  • the isochorismate synthase may be pchA
  • the isochorismate pyruvate lyase may be pchB
  • the prephenate synthase may be pheA.
  • the disruptive mutation in prephenate synthase may reduce or eliminate the expression or activity of the prephenate synthase. Such a disruptive mutation may yield a bacterium that produces a reduced amount of prephenate or prephenate-derived products compared to a parental bacterium and/or a bacterium that produces substantially no tyrosine or phenylalanine.
  • the microorganism of the invention may comprise at least one nucleic acid encoding at least one of (a) the exogenous chorismate pyruvate lyase, (b) the exogenous isochorismate synthase, (c) the exogenous isochorismate pyruvate lyase, and (d) the prephenate synthase comprising a disruptive mutation.
  • the nucleic acid is codon optimized for expression in Clostridium.
  • the chorismate-derived product may be any product produced directly or indirectly from chorismate.
  • the chorismate-derived product may comprise a 6-membered carbon ring, for example, a benzene or cyclohexane ring, substituted with a carboxyl group or carboxylate anion and further substituted with one or more OH groups and/or one or more NH 2 groups.
  • Chorismate-derived products include, but are not limited to, para-hydroxybenzoic acid, salicylate, 2-aminobenzoate, dihydroxybenzoate, and 4-hydroxycyclohexane carboxylic acid.
  • the microorganism of the invention expresses a chorismate pyruvate lyase of ubiC and produces a chorismate-derived product of para-hydroxybenzoic acid. In one embodiment the microorganism of the invention further expresses feedback-insensitive DAHP synthase.
  • the microorganism of the invention expresses an isochorismate synthase of pchA and an isochorismate pyruvate lyase of pchB and produces a chorismate-derived product of salicylate. In one embodiment the microorganism of the invention further expresses feedback-insensitive DAHP synthase.
  • the microorganism of the invention comprises a prephenate synthase comprising a disruptive mutation and produces a one or more of chorismate-derived product of 2-aminobenzoate, 2,3-dihydroxybenzoate, 3,4-dihydroxybenzoate and 4-hydroxycyclohexane carboxylic acid.
  • the microorganism of the invention produces at least one chorismate-derived product not produced by a parental microorganism or a greater amount of at least one chorismate-derived product than a parental microorganism.
  • the bacterium of the invention is derived from a C1-fixing parental bacterium.
  • the bacterium of the invention is derived from a parental bacterium selected from the group consisting of Clostridium autoethanogenum, Clostridium ljungdahlii , and Clostridium ragsdalei .
  • the bacterium of the invention is derived from a parental bacterium of Clostridium autoethanogenum deposited under DSMZ accession number DSM23693.
  • the invention further provides a method of producing a fermentation product, comprising fermenting the microorganism of the invention in the presence of a C1-containing gaseous substrate.
  • the fermentation product is a chorismate-derived product.
  • the gaseous substrate comprises at least one C1 carbon source.
  • FIG. 1 is a diagram showing production of chorismate via a native shikimate pathway in Clostridia.
  • FIG. 2 is a diagram showing the pathway for production of pHBA in a genetically engineered Clostridium bacterium.
  • FIG. 3 is a diagram showing the pathway for production of salicylate in a genetically engineered Clostridium bacterium.
  • FIG. 4 is a diagram showing the pathway for production of aromatic products in a genetically engineered Clostridium bacterium comprising a disruptive mutation in a nucleic acid encoding pheA.
  • FIG. 5 is a graph of a standard curve showing quantitation of authentic pHBA standards.
  • FIG. 6 a is a graph showing the total ion count of authentic standards (i) authentic standard of pHBA (trimethylsilyated) prepared in supernatant from C. autoethanogenum LZ1561 culture medium, (ii) authentic standard of pHBA (trimethylsilyated) prepared in water, and (iii) mass spectrum of trimethylsilyated pHBA.
  • FIG. 6 b is a graph showing selected ion monitoring of fermentation samples and standards: (i) C. autoethanogenum LZ1561 without pARO_01 plasmid, (ii) and (iii) samples from C. autoethanogenum LZ1561 bearing pARO_01 plasmid, (iv) authentic standard of pHBA, and (v) total ion count comparison between NIST database entry for pHBA and pHBA peak from LZ1561/pARO_01.
  • FIG. 7 is a diagram of a pARO_01 plasmid.
  • the chorismate pyruvate lyase (ubiC) and feedback-insensitive DAHP synthase (aroG*) are under control of the Wood-Ljungdahl promoter (Pwl).
  • Other shuttle vector features are also shown.
  • LZ1561 refers to untransformed C. autoethanogenum LZ1561.
  • pARO_01(1) and pARO_01(2) are biological replicates of C. autoethanogenum LZ1561 transformed with the pARO_01 plasmid.
  • FIGS. 9 a and 9 b are graphs showing p-hydroxybenzoate accumulation in test strains.
  • FIG. 9 a shows quantification of pHBA detected in each sample at 24, 96, 144, and 192 hour time points.
  • Three replicate cultures were sampled for the negative control strain ( C. autoethanogenum LZ1561) and the two biological replicates of C. autoethanogenum LZ1561 carrying pARO_01.
  • FIG. 10 is a graph showing production of new aromatic compounds in a genetically engineered Clostridium bacterium comprising a disruptive mutation in a nucleic acid encoding pheA.
  • the ⁇ pheA strain produces 4-hydroxy cyclohexane carboxylic acid, 2-aminobenzoic acid, and 3,4-dihydroxybenzoic acid, while the control strain (LZ1561) does not.
  • FIG. 11 a is a graph showing biomass growth of the salicylate production strain with and without induction of the salicylate biosynthetic pathway.
  • FIG. 11 b is a graph showing the difference in accumulation of salicylate in liquid cultures of the test strain with and without induction of the salicylate biosynthetic pathway.
  • FIG. 12 is a graph showing concentration of 4-hydroxy cyclohexane carboxylic acid, 2-aminobenzoic acid, and 3,4-dihydroxybenzoic acid produced by fermentation of an engineered Clostridium bacterium comprising a disruptive mutation in a nucleic acid encoding pheA.
  • FIG. 13 is a table identifying exemplary sources of chorismate pyruvate lyase (EC 4.1.3.40).
  • FIG. 14 is a table identifying exemplary sources of isochorismate synthase (EC 5.4.4.2).
  • FIG. 15 is table of identifying exemplary sources of isochorismate pyruvate lyase (EC 4.2.99.21).
  • Clostridia natively produce chorismate which serves as a precursor to the aromatic amino acids tryptophan, tyrosine, and phenylalanine, from phosphoenolpyruvate and erythrose-4-phosphate via the shikimate pathway ( FIG. 1 ). This pathway is described in detail in Bentley, Crit Rev Biochem Mol Biol, 25.5: 307-384, 1990.
  • the invention provides a genetically engineered bacterium capable of producing at least one chorismate-derived product by fermentation of a gaseous substrate.
  • the inventors have demonstrated that chorismate-derived products can be sustainably produced and recovered from a C1-carbon source.
  • the invention provides a method of producing at least one chorismate-derived product using a C1-containing gaseous substrate as the main carbon and energy source.
  • the present invention has a number of advantages over processes that rely on sugar- or cellulose-based substrates.
  • sugar- or cellulose-based substrates are typically also useful for food (e.g. sugar cane) and their intensive land use has negative environmental consequences.
  • the invention provides an alternative method for the production of chorismate-derived products, optionally via the use of waste gases (e.g. CO from industrial processes).
  • waste gases e.g. CO from industrial processes.
  • the invention provides a source of revenue from waste gases and, furthermore, captures the carbon in those waste gases to reduce the carbon emissions that would occur if the gases were flared to the atmosphere.
  • Heterotrophic microorganisms such as E. coli and S. cerevisiae produce relatively high levels of ATP through glycolysis.
  • microorganisms which use C1-carbon sources e.g., CO or CO 2
  • C1-carbon sources e.g., CO or CO 2
  • analysis of the reaction kinetics in a typical carboxydotrophic microorganism C. autoethanogenum gives a predicted ATP yield when producing pHBA, a chorismate-derived product) of ⁇ 0.4 ATP per mol of CO fixed. As such, it would not be expected that any pHBA would be produced due to the energy constraints.
  • chorismate-derived products would be produced by a carboxydotrophic microorganism due to the metabolic burden of producing such compounds under autotrophic conditions.
  • the inventors have surprisingly shown however that a number of chorismate-derived products can be produced from a gaseous substrate. Further, said products can be produced from industrial waste gases which provide practical, economic, and environmental benefits over other substrates.
  • the invention provides genetically engineered microorganisms capable of producing at least one chorismate-derived product by introducing at least one of (a) a nucleic acid encoding an exogenous chorismate pyruvate lyase, (b) a nucleic acid encoding an exogenous isochorismate synthase (a.k.a., isochorismate mutase), (c) a nucleic acid encoding an exogenous isochorismate pyruvate lyase, and (d) a nucleic acid encoding a prephenate synthase comprising a disruptive mutation.
  • a nucleic acid encoding an exogenous chorismate pyruvate lyase a nucleic acid encoding an exogenous isochorismate synthase (a.k.a., isochorismate mutase)
  • the genetically engineered microorganism is a C1-fixing bacterium capable of producing at least one chorismate-derived product by fermentation of a gaseous substrate.
  • the C1-fixing bacterium is a Clostridium bacterium.
  • Chorismate-derived product or “product derived from chorismate” or similar terms encompass products produced directly or indirectly from chorismate (or chorismic acid).
  • Chorismate-derived products typically comprise a 6-membered carbon ring, for example, a benzene or cyclohexane ring, substituted with a carboxyl group or carboxylate anion and further substituted with one or more OH groups and/or one or more NH2 groups.
  • chorismate-derived products include, but are not limited to, para-hydroxybenzoic acid, salicylate, 2-aminobenzoate, 2,3-dihydroxybenzoate, 3,4-dihydroxybenzoate, and 4-hydroxycyclohexane carboxylic acid.
  • the microorganism of the invention may comprise an exogenous chorismate pyruvate lyase enzyme (EC 4.1.3.40) that catalyzes the conversion of chorismate to para-hydroxybenzoic acid and pyruvate in the first committed step of ubiquinone biosynthesis.
  • the enzyme may be derived from any microorganism having such an enzyme.
  • the enzyme may be a UbiC enzyme.
  • the UbiC enzyme may be derived from Escherichia coli, Klebsiella oxytoca, Citrobacter freundii , or any other microorganism having a UbiC enzyme.
  • the UbiC enzyme is derived from Escherichia coli and comprises SEQ ID NO: 1 or a functionally equivalent variant thereof.
  • the microorganism of the invention may comprise a nucleic acid encoding an exogenous chorismate pyruvate lyase.
  • the nucleic acid may be a chorismate pyruvate lyase gene derived from any microorganism having such a gene.
  • the chorismate pyruvate lyase gene may be a ubiC gene.
  • the ubiC gene may be derived from Escherichia coli, Klebsiella oxytoca, Citrobacter freundii , or any other microorganism having a ubiC gene.
  • the ubiC gene is derived from Escherichia coli and comprises SEQ ID NO: 2 or a codon-optimized or functionally equivalent variant thereof.
  • the UbiC enzyme or ubiC gene may also be modified (e.g., mutated) to enhance solubility, stability, or other gene/enzyme properties. Such modifications may result in increased product titers.
  • Example 4 describes an experimental protocol to engineer a UbiC enzyme to decrease product inhibition through retention of para-hydroxybenzoic acid.
  • One particular modification involves engineering the ubiC gene to express a UbiC enzyme with two surface-active serines instead of cysteines. The serine residues result in less protein aggregation and, in turn, improved solubility.
  • the UbiC enzyme comprises a mutation to replace at least one surface-active cysteine with a serine.
  • the chorismate pyruvate lyase (EC 4.1.3.40) may be or may be derived, for example, from any of the sources identified in FIG. 13 .
  • an exogenous chorismate pyruvate lyase e.g., ubiC
  • a nucleic acid encoding an exogenous chorismate pyruvate lyase e.g., ubiC
  • the production of para-hydroxybenzoic acid is illustrated in FIG. 2 .
  • C1 fixing bacteria including the species Acetobacterium woodii, Alkalibaculum bacchii, Blautia producta, Butyribacterium methylotrophicum, Clostridium aceticum, Clostridium autoethanogenum, Clostridium carboxidivorans, Clostridium coskatii, Clostridium drakei, Clostridium formicoaceticum, Clostridium ljungdahlii, Clostridium magnum, Clostridium ragsdalei, Clostridium scatologenes, Eubacterium limosum, Moorella thermautotrophica, Moorella thermoacetica, Oxobacter pfennigii, Sporomusa ovata, Sporomusa silvacetica, Sporomusa sphaeroides , and Thermoanaerobacter kivui , do not natively produce para-hydroxybenzoic acid.
  • Para-hydroxybenzoic acid may also be referred to, for example, as pHBA, 4-hydroxybenzoic acid, p-hydroxybenzoic acid, or para-hydroxybenzoate. References to any of these terms, as used herein, encompass both the acid and anion forms of the molecule.
  • the microorganism of the invention may comprise an exogenous isochorismate synthase enzyme, also referred to as isochorismate mutase, (EC 5.4.4.2) that catalyzes the conversion of chorismate to isochorismate.
  • the enzyme may be derived from any microorganism having such an enzyme.
  • the enzyme may be a PchA enzyme.
  • the PchA enzyme may be derived from Pseudomonas aeruginosa or any other microorganism having a PchA enzyme.
  • the PchA enzyme is derived from Pseudomonas aeruginosa and comprises SEQ ID NO: 3 or a functionally equivalent variant thereof.
  • the microorganism of the invention may comprise a nucleic acid encoding an exogenous isochorismate synthase.
  • the nucleic acid may be an isochorismate synthase gene derived from any microorganism having such a gene.
  • the isochorismate synthase gene may be a pchA gene.
  • the pchA gene may be derived from Pseudomonas aeruginosa or any other microorganism having a pchA gene.
  • the pchA gene is derived from Pseudomonas aeruginosa and comprises SEQ ID NO: 4 or a codon-optimized or functionally equivalent variant thereof.
  • the isochorismate synthase (EC 5.4.4.2) may be or may be derived, for example, from any of the sources identified in FIG. 14 .
  • the microorganism of the invention may comprise an exogenous isochorismate pyruvate lyase enzyme (EC 4.2.99.21) that catalyzes the conversion of isochorismate to salicylate and pyruvate.
  • the enzyme may be derived from any microorganism having such an enzyme.
  • the enzyme may be a PchB enzyme.
  • the PchB enzyme may be derived from Pseudomonas aeruginosa or any other microorganism having a PchB enzyme.
  • the PchB enzyme is derived from Pseudomonas aeruginosa and comprises SEQ ID NO: 5 or a functionally equivalent variant thereof.
  • the microorganism of the invention may comprise a nucleic acid encoding an exogenous isochorismate pyruvate lyase.
  • the nucleic acid may be an isochorismate pyruvate lyase gene derived from any microorganism having such a gene.
  • the isochorismate pyruvate lyase gene may be a pchB gene.
  • the pchB gene may be derived from Pseudomonas aeruginosa or any other microorganism having a pchB gene.
  • the pchB gene is derived from Pseudomonas aeruginosa and comprises SEQ ID NO: 6 or a codon-optimized or functionally equivalent variant thereof.
  • the isochorismate pyruvate lyase (EC 4.2.99.21) may be or may be derived, for example, from any of the sources identified in FIG. 15 .
  • an exogenous isochorismate synthase e.g., pchA
  • an exogenous isochorismate pyruvate lyase e.g., pchB
  • FIG. 3 The production of salicylate is illustrated in FIG. 3 , whereby chorismate is converted to isochorismate by isochorismate synthase and then further converted to salicylate and pyruvate by isochorismate pyruvate lyase.
  • C1 fixing bacteria including the species Acetobacterium woodii, Alkalibaculum bacchii, Blautia producta, Butyribacterium methylotrophicum, Clostridium aceticum, Clostridium autoethanogenum, Clostridium carboxidivorans, Clostridium coskatii, Clostridium drakei, Clostridium formicoaceticum, Clostridium ljungdahlii, Clostridium magnum, Clostridium ragsdalei, Clostridium scatologenes, Eubacterium limosum, Moorella thermautotrophica, Moorella thermoacetica, Oxobacter pfennigii, Sporomusa ovata, Sporomusa silvacetica, Sporomusa sphaeroides , and Thermoanaerobacter kivui , do not natively produce salicylate.
  • Salicylate may also be referred to, for example, as 2-hydroxybenzoate, salicylic acid, or 2-hydroxybenzoic acid. References to any of these terms, as used herein, encompass both the acid and anion forms of the molecule.
  • the microorganism of the invention may comprise a prephenate synthase enzyme (EC 5.4.99.5) comprising a disruptive mutation.
  • Prephenate synthase typically catalyzes the conversion of chorismate to prephenate (i.e., a chorismate ⁇ prephenate mutase reaction). Accordingly, a prephenate synthase enzyme comprising a disruptive mutation is unable or less able to catalyze the conversion of chorismate to prephenate.
  • the prephenate synthase comprising a disruptive mutation may be pheA comprising a disruptive mutation.
  • the prephenate synthase may also be referred to as chorismate mutase.
  • the pheA may be a bifunctional enzyme that carries out both prephenate synthase (i.e., chorismate mutase) (EC 5.4.99.5) and prephenate dehydratase (EC 4.2.1.51) reactions. In microorganisms where these two reactions are carried out by separate enzymes, knocking out EC 5.4.99.5 activity will result in significantly decreased or eliminated production of prephenate or compounds downstream of prephenate, while knocking out EC 4.2.1.51 activity alone would not achieve the same phenotype, since prephenate may still be produced.
  • the pheA is derived from Clostridium autoethanogenum and comprises SEQ ID NO: 11 or a functionally equivalent variant thereof
  • the microorganism of the invention may comprise a nucleic acid encoding a prephenate synthase comprising a disruptive mutation.
  • the nucleic acid may be a pheA gene comprising a disruptive mutation.
  • the disruptive mutation is a knockout mutation of a pheA gene.
  • the pheA gene is derived from Clostridium autoethanogenum and comprises SEQ ID NO: 10 or a codon-optimized or functionally equivalent variant thereof.
  • Disrupting prephenate synthase results in reduced or eliminated production of phenylalanine and tyrosine. Surprisingly, disrupting prephenate synthase also results in the production of additional products that are not typically produced or that are produced only at very low levels.
  • prephenate synthase e.g., pheA
  • a nucleic acid encoding prephenate synthase e.g., pheA
  • production of one or more of 2-aminobenzoate, dihydroxybenzoate, and 4-hydroxycyclohexane carboxylic acid, all chorismate-derived products is illustrated in FIG. 4 .
  • Clostridia such as Clostridium autoethanogenum, Clostridium ljungdahlii , and Clostridium ragsdalei , do not natively produce these products or only produce very low levels of these products.
  • pheA Exemplary sources for pheA are provided. However, it should be appreciated that other suitable sources for pheA may be available
  • the prephenate dehydratase be or may be derived, for example, from any of the following sources, the sequences of which are publically available:
  • 2-aminobenzoate may also be referred to, for example, as 2-aminobenzoic acid, o-aminobenzoic acid, anthranilic acid, anthranilate, or vitamin L1. References to any of these terms, as used herein, encompass both the acid and anion forms of the molecule.
  • Dihydroxybenzoate may be referred to, for example, as 2,3-dihydroxybenzoate, 2,3-dihydroxybenzoic acid, 3,4-dihydroxybenzoate, 3,4-dihydroxybenzoic acid or Protocatechuic acid. References to any of these terms, as used herein, encompass both the acid and anion forms of the molecule.
  • 4-hydroxycyclohexane carboxylic acid may also be referred to, for example, as cis-4-hydroxycyclohexane carboxylic acid or 4-hydroxycyclohexane-1-carboxylate. References to any of these terms, as used herein, encompass both the acid and anion forms of the molecule.
  • the microorganism of the invention further comprises a nucleic acid encoding a feedback-insensitive DAHP synthase DAHP synthase catalyses the first committed step in the shikimate pathway ( FIG. 1 ) in which erythrose-4-phosphate and phosphoenolpyruvate are converted to 3-deoxy-D-arabinoheptosonate-7-phosphate.
  • the inventors believe that this step in the pathway is subject to feedback inhibition by aromatic amino acids (tryptophan, phenylalanine, tyrosine) as described for E. coli (Hu et al. J. Basic Microbiol. 2003, 43:399-406).
  • nucleic acids encoding appropriate DAHP synthases are known to those of skill in the art.
  • the nucleic acid encoding a DAHP synthase may be derived from Escherichia coli, Clostridium beijerinckii , or Saccharomyces cerevisiae .
  • the DAHP synthase may be feedback-insensitive DAHP synthase from Escherichia coli , having the nucleic acid sequence of SEQ ID NO: 7 and the amino acid sequence of SEQ ID NO: 8.
  • the feedback-insensitive DAHP synthase may be introduced on the same vector as a gene encoding one of the aforementioned enzymes or on a different vector.
  • the feedback-insensitive DAHP synthase may have its own promoter or may follow the promoter for one of the aforementioned enzymes in a bicistronic arrangement, wherein a single promoter drives the transcription of a single mRNA that encodes both the enzyme and the feedback-insensitive DAHP synthase.
  • the microorganism of the invention comprises an exogenous chorismate pyruvate lyase enzyme (EC 4.1.3.40), and an exogenous feedback-insensitive DAHP synthase.
  • the microorganism comprises an exogenous UbiC enzyme, and an exogenous feedback-insensitive DAHP synthase.
  • the invention comprises exogenous ubiC gene having the nucleic acid sequence of SEQ ID NO: 1, and an exogenous feedback-insensitive DAHP synthase having the nucleic acid sequence of SEQ ID NO: 7.
  • the microorganism comprising both an exogenous chorismate pyruvate lyase enzyme and an exogenous feedback-insensitive DAHP synthase demonstrates greater production of para-hydroxybenzoic acid compared to a microorganism without a feedback-insensitive DAHP synthase.
  • the microorganism of the invention may comprise a nucleic acid encoding both an exogenous chorismate pyruvate lyase and feedback-insensitive DAHP synthase.
  • the microorganism of the invention comprises (i) an exogenous isochorismate mutase, (EC 5.4.4.2), (ii) an isochorismate pyruvate lyase enzyme (EC 4.2.99.21), and (iii) an exogenous feedback-insensitive DAHP synthase.
  • the microorganism comprises an exogenous PchA enzyme, an exogenous PchB enzyme, and an exogenous feedback-insensitive DAHP synthase.
  • the microorganism comprising an exogenous feedback-insensitive DAHP synthase demonstrates greater production of salicylic acid compared to a microorganism without a feedback-insensitive DAHP synthase.
  • the microorganism of the invention may comprise a nucleic acid encoding both an exogenous chorismate pyruvate lyase and feedback-insensitive DAHP synthase.
  • the microorganism of the invention does not comprise a feedback-insensitive DAHP synthase and instead merely comprises an endogenous DAHP synthase.
  • production or natural concentration of aromatic amino acids is expected to be low enough so as to not induce feedback inhibition, it is not necessary to introduce a feedback-insensitive DAHP synthase.
  • the microorganism of the invention may produce chorismate-derived products at any concentration or in any amount.
  • the microorganism of the invention produces chorismate-derived products at a concentration of at least about 5 mg/L, 10 mg/L, 15 mg/L, 20 mg/L, 30 mg/L, 50 mg/L, 75 mg/L, 100 mg/L, 200 mg/L, 500 mg/L, 750 mg/L, 1 g/L, 1.5 g/L or 2 g/L.
  • the microorganism of the invention produces at least one chorismate-derived product at a concentration of at least 10 mg/L, 50 gm/L, 100 mg/L, 500 mg/L, 800 mg/L, or 1 g/L
  • the microorganism of the invention may be engineered to produce products at a certain selectivity or at a minimum selectivity.
  • a target chorismate-derived product accounts for at least about 5%, 10%, 15%, 20%, 30%, 50%, or 75% of all fermentation products produced by the microorganism of the invention.
  • the target chorismate-derived product accounts for at least 10% of all fermentation products produced by the microorganism of the invention, such that the microorganism of the invention has a selectivity for the target chorismate-derived product of at least 10%.
  • the target chorismate-derived product accounts for at least 30% of all fermentation products produced by the microorganism of the invention, such that the microorganism of the invention has a selectivity for the target chorismate-derived product of at least 30%.
  • the invention further provides a method of producing a fermentation product, specifically a chorismate-derived product, comprising fermenting the microorganism of the invention in the presence of a gaseous substrate.
  • the invention also provides chorismate-derived products produced by fermenting a microorganism of the invention in the presence of a gaseous substrate.
  • genetic modification or “genetic engineering” broadly refers to manipulation of the genome or nucleic acids of a microorganism. Methods of genetic modification of include, for example, heterologous gene expression, gene or promoter insertion or deletion, nucleic acid mutation, altered gene expression or inactivation, enzyme engineering, directed evolution, knowledge-based design, random mutagenesis methods, gene shuffling, and codon optimization.
  • Recombinant indicates that a nucleic acid, protein, or microorganism is the product of genetic modification, engineering, or recombination.
  • the term “recombinant” refers to a nucleic acid, protein, or microorganism that contains or is encoded by genetic material derived from multiple sources, such as two or more different strains or species of microorganisms.
  • the term “recombinant” may also be used to describe a microorganism that comprises a mutated nucleic acid or protein, including a mutated form of an endogenous nucleic acid or protein.
  • Endogenous refers to a nucleic acid or protein that is present or expressed in the wild-type or parental microorganism from which the microorganism of the invention is derived.
  • an endogenous gene is a gene that is natively present in the wild-type or parental microorganism from which the microorganism of the invention is derived.
  • the expression of an endogenous gene may be controlled by an exogenous regulatory element, such as an exogenous promoter.
  • Exogenous refers to a nucleic acid or protein that is not present in the wild-type or parental microorganism from which the microorganism of the invention is derived.
  • an exogenous gene or enzyme may be derived from a heterologous (i.e., different) strain or species and introduced to or expressed in the microorganism of the invention.
  • an exogenous gene or enzyme may be artificially or recombinantly created and introduced to or expressed in the microorganism of the invention.
  • Exogenous nucleic acids may be adapted to integrate into the genome of the microorganism of the invention or to remain in an extra-chromosomal state in the microorganism of the invention, for example, in a plasmid.
  • Enzyme activity refers broadly to enzymatic activity, including, but not limited, to the activity of an enzyme, the amount of an enzyme, or the availability of an enzyme to catalyze a reaction. Accordingly, “increasing” enzyme activity includes increasing the activity of an enzyme, increasing the amount of an enzyme, or increasing the availability of an enzyme to catalyze a reaction.
  • “Mutated” refers to a nucleic acid or protein that has been modified in the microorganism of the invention compared to the wild-type or parental microorganism from which the microorganism of the invention is derived.
  • the mutation may be a deletion, insertion, or substitution in a gene encoding an enzyme.
  • the mutation may be a deletion, insertion, or substitution of one or more amino acids in an enzyme.
  • a “disruptive mutation” is a mutation that reduces or eliminates (i.e., “disrupts”) the expression or activity of a gene or enzyme.
  • the disruptive mutation may partially inactivate, fully inactivate, or delete the gene or enzyme.
  • the disruptive mutation may be a knockout (KO) mutation.
  • the disruptive mutation may be any mutation that reduces, prevents, or blocks the biosynthesis of a product produced by an enzyme.
  • the disruptive mutation may include, for example, a mutation in a gene encoding an enzyme, a mutation in a genetic regulatory element involved in the expression of a gene encoding an enzyme, the introduction of a nucleic acid which produces a protein that reduces or inhibits the activity of an enzyme, or the introduction of a nucleic acid (e.g., antisense RNA, siRNA, CRISPR) or protein which inhibits the expression of an enzyme.
  • the disruptive mutation may be introduced using any method known in the art.
  • Codon optimization refers to the mutation of a nucleic acid, such as a gene, for optimized or improved translation of the nucleic acid in a particular strain or species. Codon optimization may result in faster translation rates or higher translation accuracy.
  • the genes of the invention are codon optimized for expression in Clostridium , particularly Clostridium autoethanogenum, Clostridium ljungdahlii , or Clostridium ragsdalei .
  • the genes of the invention are codon optimized for expression in Clostridium autoethanogenum LZ1561, which is deposited under DSMZ accession number DSM23693.
  • “Overexpressed” refers to an increase in expression of a nucleic acid or protein in the microorganism of the invention compared to the wild-type or parental microorganism from which the microorganism of the invention is derived. Overexpression may be achieved by any means known in the art, including modifying gene copy number, gene transcription rate, gene translation rate, or enzyme degradation rate.
  • variants includes nucleic acids and proteins whose sequence varies from the sequence of a reference nucleic acid and protein, such as a sequence of a reference nucleic acid and protein disclosed in the prior art or exemplified herein.
  • the invention may be practiced using variant nucleic acids or proteins that perform substantially the same function as the reference nucleic acid or protein.
  • a variant protein may perform substantially the same function or catalyze substantially the same reaction as a reference protein.
  • a variant gene may encode the same or substantially the same protein as a reference gene.
  • a variant promoter may have substantially the same ability to promote the expression of one or more genes as a reference promoter.
  • nucleic acids or proteins may be referred to herein as “functionally equivalent variants.”
  • functionally equivalent variants of a nucleic acid may include allelic variants, fragments of a gene, mutated genes, polymorphisms, and the like.
  • Homologous genes from other microorganisms are also examples of functionally equivalent variants. These include homologous genes in species such as Clostridium acetobutylicum, Clostridium beijerinckii , or Clostridium ljungdahlii , the details of which are publicly available on websites such as Genbank or NCBI.
  • Functionally equivalent variants also include nucleic acids whose sequence varies as a result of codon optimization for a particular microorganism.
  • a functionally equivalent variant of a nucleic acid will preferably have at least approximately 70%, approximately 80%, approximately 85%, approximately 90%, approximately 95%, approximately 98%, or greater nucleic acid sequence identity (percent homology) with the referenced nucleic acid.
  • a functionally equivalent variant of a protein will preferably have at least approximately 70%, approximately 80%, approximately 85%, approximately 90%, approximately 95%, approximately 98%, or greater amino acid identity (percent homology) with the referenced protein.
  • the functional equivalence of a variant nucleic acid or protein may be evaluated using any method known in the art.
  • Nucleic acids may be delivered to a microorganism of the invention using any method known in the art.
  • nucleic acids may be delivered as naked nucleic acids or may be formulated with one or more agents, such as liposomes.
  • the nucleic acids may be DNA, RNA, cDNA, or combinations thereof, as is appropriate. Restriction inhibitors may be used in certain embodiments.
  • Additional vectors may include plasmids, viruses, bacteriophages, cosmids, and artificial chromosomes.
  • nucleic acids are delivered to the microorganism of the invention using a plasmid.
  • transformation including transduction or transfection
  • transformation may be achieved by electroporation, ultrasonication, polyethylene glycol-mediated transformation, chemical or natural competence, protoplast transformation, prophage induction, or conjugation.
  • active restriction enzyme systems it may be necessary to methylate a nucleic acid before introduction of the nucleic acid into a microorganism.
  • nucleic acids may be designed to comprise a regulatory element, such as a promoter, to increase or otherwise control expression of a particular nucleic acid.
  • the promoter may be a constitutive promoter or an inducible promoter.
  • the promoter is a Wood-Ljungdahl pathway promoter, a ferredoxin promoter, a pyruvate:ferredoxin oxidoreductase promoter, an Rnf complex operon promoter, an ATP synthase operon promoter, or a phosphotransacetylase/acetate kinase operon promoter.
  • microorganism is a microscopic organism, especially a bacterium, archea, virus, or fungus.
  • the microorganism of the invention is typically a bacterium.
  • recitation of “microorganism” should be taken to encompass “bacterium.”
  • a “parental microorganism” is a microorganism used to generate a microorganism of the invention.
  • the parental microorganism may be a naturally-occurring microorganism (i.e., a wild-type microorganism) or a microorganism that has been previously modified (i.e., a mutant or recombinant microorganism).
  • the microorganism of the invention may be modified to express or overexpress one or more enzymes that were not expressed or overexpressed in the parental microorganism.
  • the microorganism of the invention may be modified to contain one or more genes that were not contained by the parental microorganism.
  • the parental microorganism is Clostridium autoethanogenum, Clostridium ljungdahlii , or Clostridium ragsdalei .
  • the parental microorganism is Clostridium autoethanogenum LZ1561, which is deposited under DSMZ accession DSM23693.
  • the term “derived from” indicates that a nucleic acid, protein, or microorganism is modified or adapted from a different (e.g., a parental or wild-type) nucleic acid, protein, or microorganism, so as to produce a new nucleic acid, protein, or microorganism. Such modifications or adaptations typically include insertion, deletion, mutation, or substitution of nucleic acids or genes.
  • the microorganism of the invention is derived from a parental microorganism.
  • the microorganism of the invention is derived from Clostridium autoethanogenum, Clostridium ljungdahlii , or Clostridium ragsdalei .
  • the microorganism of the invention is derived from Clostridium autoethanogenum LZ1561, which is deposited under DSMZ accession DSM23693.
  • the microorganism of the invention may be further classified based on functional characteristics.
  • the microorganism of the invention may be or may be derived from a C1-fixing microorganism, an anaerobe, an acetogen, an ethanologen, a carboxydotroph, and/or a methanogen.
  • Table 1 provides a representative list of microorganisms and identifies their functional characteristics.
  • C1 refers to a one-carbon molecule, for example, CO, CO 2 , CH 4 , or CH 3 OH.
  • C1-oxygenate refers to a one-carbon molecule that also comprises at least one oxygen atom, for example, CO, CO 2 , or CH 3 OH.
  • C1-carbon source refers a one carbon-molecule that serves as a partial or sole carbon source for the microorganism of the invention.
  • a C1-carbon source may comprise one or more of CO, CO 2 , CH 4 , CH 3 OH, or CH 2 O 2 .
  • the C1-carbon source comprises one or both of CO and CO 2 .
  • a “C1-fixing microorganism” is a microorganism that has the ability to produce one or more products from a C1-carbon source.
  • the microorganism of the invention is a C1-fixing bacterium.
  • the microorganism of the invention is derived from a C1-fixing microorganism identified in Table 1.
  • an “anaerobe” is a microorganism that does not require oxygen for growth. An anaerobe may react negatively or even die if oxygen is present. Typically, the microorganism of the invention is an anaerobe. In a preferred embodiment, the microorganism of the invention is derived from an anaerobe identified in Table 1.
  • acetogen is a microorganism that produces or is capable of producing acetate (or acetic acid) as a product of anaerobic respiration.
  • acetogens are obligately anaerobic bacteria that use the Wood-Ljungdahl pathway as their main mechanism for energy conservation and for synthesis of acetyl-CoA and acetyl-CoA-derived products, such as acetate (Ragsdale, Biochim Biophys Acta, 1784: 1873-1898, 2008).
  • Acetogens use the acetyl-CoA pathway as a (1) mechanism for the reductive synthesis of acetyl-CoA from CO 2 , (2) terminal electron-accepting, energy conserving process, (3) mechanism for the fixation (assimilation) of CO 2 in the synthesis of cell carbon (Drake, Acetogenic Prokaryotes, In: The Prokaryotes, 3rd edition, p. 354, New York, N.Y., 2006). All naturally occurring acetogens are C1-fixing, anaerobic, autotrophic, and non-methanotrophic.
  • the microorganism of the invention is an acetogen.
  • the microorganism of the invention is derived from an acetogen identified in Table 1.
  • an “ethanologen” is a microorganism that produces or is capable of producing ethanol.
  • the microorganism of the invention is an ethanologen.
  • the microorganism of the invention is derived from an ethanologen identified in Table 1.
  • an “autotroph” is a microorganism capable of growing in the absence of organic carbon. Instead, autotrophs use inorganic carbon sources, such as CO and/or CO 2 .
  • the microorganism of the invention is an autotroph.
  • the microorganism of the invention is derived from an autotroph identified in Table 1.
  • a “carboxydotroph” is a microorganism capable of utilizing CO as a sole source of carbon.
  • the microorganism of the invention is a carboxydotroph.
  • the microorganism of the invention is derived from a carboxydotroph identified in Table 1.
  • a “methanotroph” is a microorganism capable of utilizing methane as a sole source of carbon and energy.
  • the microorganism of the invention is derived from a methanotroph.
  • the microorganism of the invention may be derived from any genus or species identified in Table 1.
  • the microorganism of the invention is a Clostridium bacterium.
  • the microorganism of the invention is derived from the cluster of Clostridia comprising the species Clostridium autoethanogenum, Clostridium ljungdahlii , and Clostridium ragsdalei . These species were first reported and characterized by Abrini, Arch Microbiol, 161: 345-351, 1994 ( Clostridium autoethanogenum ), Tanner, Int J System Bacteriol, 43: 232-236, 1993 ( Clostridium ljungdahlii ), and Huhnke, WO 2008/028055 ( Clostridium ragsdalei ).
  • these species are clustered in clostridial rRNA homology group I with 16S rRNA DNA that is more than 99% identical, have a DNA G+C content of about 22-30 mol %, are gram-positive, have similar morphology and size (logarithmic growing cells between 0.5-0.7 ⁇ 3-5 ⁇ m), are mesophilic (grow optimally at 30-37° C.), have similar pH ranges of about 4-7.5 (with an optimal pH of about 5.5-6), lack cytochromes, and conserve energy via an Rnf complex. Also, reduction of carboxylic acids into their corresponding alcohols has been shown in these species (Perez, Biotechnol Bioeng, 110:1066-1077, 2012). Importantly, these species also all show strong autotrophic growth on CO-containing gases, produce ethanol and acetate (or acetic acid) as main fermentation products, and produce small amounts of 2,3-butanediol and lactic acid under certain conditions.
  • Clostridium autoethanogenum from rabbit gut Clostridium ljungdahlii from chicken yard waste
  • Clostridium ragsdalei from freshwater sediment.
  • These species differ in utilization of various sugars (e.g., rhamnose, arabinose), acids (e.g., gluconate, citrate), amino acids (e.g., arginine, histidine), and other substrates (e.g., betaine, butanol).
  • these species differ in auxotrophy to certain vitamins (e.g., thiamine, biotin).
  • Wood-Ljungdahl pathway genes and proteins have differences in nucleic and amino acid sequences of Wood-Ljungdahl pathway genes and proteins, although the general organization and number of these genes and proteins has been found to be the same in all species (Kopke, Curr Opin Biotechnol, 22: 320-325, 2011).
  • Clostridium autoethanogenum many of the characteristics of Clostridium autoethanogenum, Clostridium ljungdahlii , or Clostridium ragsdalei are not specific to that species, but are rather general characteristics for this cluster of C1-fixing, anaerobic, acetogenic, ethanologenic, and carboxydotrophic members of the genus Clostridium .
  • these species are, in fact, distinct, the genetic modification or manipulation of one of these species may not have an identical effect in another of these species. For instance, differences in growth, performance, or product production may be observed.
  • the microorganism of the invention may also be derived from an isolate or mutant of Clostridium autoethanogenum, Clostridium ljungdahlii , or Clostridium ragsdalei .
  • Isolates and mutants of Clostridium autoethanogenum include JA1-1 (DSM10061) (Abrini, Arch Microbiol, 161: 345-351, 1994), LBS1560 (DSM19630) (WO 2009/064200), and LZ1561 (DSM23693).
  • Isolates and mutants of Clostridium ljungdahlii include ATCC 49587 (Tanner, Int J Syst Bacteriol, 43: 232-236, 1993), PETCT (DSM13528, ATCC 55383), ERI-2 (ATCC 55380) (U.S. Pat. No. 5,593,886), C-01 (ATCC 55988) (U.S. Pat. No. 6,368,819), O-52 (ATCC 55989) (U.S. Pat. No. 6,368,819), and OTA-1 (Tirado-Acevedo, Production of bioethanol from synthesis gas using Clostridium ljungdahlii , PhD thesis, North Carolina State University, 2010).
  • Isolates and mutants of Clostridium ragsdalei include PI 1 (ATCC BAA-622, ATCC PTA-7826) (WO 2008/028055).
  • “Substrate” refers to a carbon and/or energy source for the microorganism of the invention.
  • the substrate is gaseous and comprises a C1-carbon source, for example, CO, CO 2 , and/or CH 4 .
  • the substrate comprises a C1-carbon source of CO or CO+CO 2 .
  • the substrate may further comprise other non-carbon components, such as H 2 , N 2 , or electrons.
  • the substrate generally comprises at least some amount of CO, such as about 1, 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 mol % CO.
  • the substrate may comprise a range of CO, such as about 20-80, 30-70, or 40-60 mol % CO.
  • the substrate comprises about 40-70 mol % CO (e.g., steel mill or blast furnace gas), about 20-30 mol % CO (e.g., basic oxygen furnace gas), or about 15-45 mol % CO (e.g., syngas).
  • the substrate may comprise a relatively low amount of CO, such as about 1-10 or 1-20 mol % CO.
  • the microorganism of the invention typically converts at least a portion of the CO in the substrate to a product.
  • the substrate may comprise some amount of H 2 .
  • the substrate may comprise about 1, 2, 5, 10, 15, 20, or 30 mol % H 2 .
  • the substrate may comprise a relatively high amount of H2, such as about 60, 70, 80, or 90 mol % H 2 .
  • the substrate comprises substantially no H 2 .
  • the substrate may comprise some amount of CO 2 .
  • the substrate may comprise about 1-80 or 1-30 mol % CO 2 .
  • the substrate may comprise less than about 20, 15, 10, or 5 mol % CO 2 .
  • the substrate comprises substantially no CO 2 .
  • the substrate is typically gaseous
  • the substrate may also be provided in alternative forms.
  • the substrate may be dissolved in a liquid saturated with a CO-containing gas using a microbubble dispersion generator.
  • the substrate may be adsorbed onto a solid support.
  • the substrate and/or C1-carbon source may be a waste gas obtained as a byproduct of an industrial process or from some other source, such as from automobile exhaust fumes or biomass gasification.
  • the industrial process is selected from the group consisting of ferrous metal products manufacturing, such as a steel mill manufacturing, non-ferrous products manufacturing, petroleum refining processes, coal gasification, electric power production, carbon black production, ammonia production, methanol production, and coke manufacturing.
  • the substrate and/or C1-carbon source may be captured from the industrial process before it is emitted into the atmosphere, using any convenient method.
  • the substrate and/or C1-carbon source may be syngas, such as syngas obtained by gasification of coal or refinery residues, gasification of biomass, or reforming of natural gas.
  • the composition of the substrate may have a significant impact on the efficiency and/or cost of the reaction. For example, the presence of oxygen (02) may reduce the efficiency of an anaerobic fermentation process.
  • it may be desirable to treat, scrub, or filter the substrate to remove any undesired impurities, such as toxins, undesired components, or dust particles, and/or increase the concentration of desirable components.
  • the microorganism of the invention may be cultured to produce one or more products.
  • Clostridium autoethanogenum produces or can be engineered to produce ethanol (WO 2007/117157), acetate (WO 2007/117157), butanol (WO 2008/115080 and WO 2012/053905), butyrate (WO 2008/115080), 2,3-butanediol (WO 2009/151342), lactate (WO 2011/112103), butene (WO 2012/024522), butadiene (WO 2012/024522), methyl ethyl ketone (2-butanone) (WO 2012/024522 and WO 2013/185123), ethylene (WO 2012/026833), acetone (WO 2012/115527), isopropanol (WO 2012/115527), lipids (WO 2013/036147), 3-hydroxypropionate (3-HP) (WO 2013/180581), isoprene (WO 2013/180584), fatty acids (WO 2013/191567), 2-butanol (
  • “Selectivity” refers to the ratio of the production of a target product to the production of all fermentation products produced by a microorganism.
  • the microorganism of the invention may be engineered to produce products at a certain selectivity or at a minimum selectivity.
  • a target product account for at least about 5%, 10%, 15%, 20%, 30%, 50%, or 75% of all fermentation products produced by the microorganism of the invention.
  • the target product accounts for at least 10% of all fermentation products produced by the microorganism of the invention, such that the microorganism of the invention has a selectivity for the target product of at least 10%.
  • the target product accounts for at least 30% of all fermentation products produced by the microorganism of the invention, such that the microorganism of the invention has a selectivity for the target product of at least 30%.
  • the culture is performed in a bioreactor.
  • the term “bioreactor” includes a culture/fermentation device consisting of one or more vessels, towers, or piping arrangements, such as a continuous stirred tank reactor (CSTR), immobilized cell reactor (ICR), trickle bed reactor (TBR), bubble column, gas lift fermenter, static mixer, or other vessel or other device suitable for gas-liquid contact.
  • the bioreactor may comprise a first growth reactor and a second culture/fermentation reactor.
  • the substrate may be provided to one or both of these reactors.
  • the terms “culture” and “fermentation” are used interchangeably. These terms encompass both the growth phase and product biosynthesis phase of the culture/fermentation process.
  • the culture is generally maintained in an aqueous culture medium that contains nutrients, vitamins, and/or minerals sufficient to permit growth of the microorganism.
  • the aqueous culture medium is an anaerobic microbial growth medium, such as a minimal anaerobic microbial growth medium. Suitable media are well known in the art.
  • the culture/fermentation should desirably be carried out under appropriate conditions for production of the target product.
  • Reaction conditions to consider include pressure (or partial pressure), temperature, gas flow rate, liquid flow rate, media pH, media redox potential, agitation rate (if using a continuous stirred tank reactor), inoculum level, maximum gas substrate concentrations to ensure that gas in the liquid phase does not become limiting, and maximum product concentrations to avoid product inhibition.
  • the rate of introduction of the substrate may be controlled to ensure that the concentration of gas in the liquid phase does not become limiting, since products may be consumed by the culture under gas-limited conditions.
  • a bioreactor at elevated pressures allows for an increased rate of gas mass transfer from the gas phase to the liquid phase. Accordingly, it is generally preferable to perform the culture/fermentation at pressures higher than atmospheric pressure. Also, since a given gas conversion rate is, in part, a function of the substrate retention time and retention time dictates the required volume of a bioreactor, the use of pressurized systems can greatly reduce the volume of the bioreactor required and, consequently, the capital cost of the culture/fermentation equipment. This, in turn, means that the retention time, defined as the liquid volume in the bioreactor divided by the input gas flow rate, can be reduced when bioreactors are maintained at elevated pressure rather than atmospheric pressure. The optimum reaction conditions will depend partly on the particular microorganism used.
  • Target products may be separated or purified from a fermentation broth using any method or combination of methods known in the art, including, for example, fractional distillation, evaporation, pervaporation, gas stripping, phase separation, and extractive fermentation, including for example, liquid-liquid extraction.
  • target products are recovered from the fermentation broth by continuously removing a portion of the broth from the bioreactor, separating microbial cells from the broth (conveniently by filtration), and recovering one or more target products from the broth.
  • Alcohols and/or acetone may be recovered, for example, by distillation.
  • Acids may be recovered, for example, by adsorption on activated charcoal.
  • Separated microbial cells are preferably returned to the bioreactor.
  • the cell-free permeate remaining after target products have been removed is also preferably returned to the bioreactor. Additional nutrients (such as B vitamins) may be added to the cell-free permeate to replenish the medium before it is returned to the bioreactor.
  • This example describes general methods for culturing C. autoethanogenum and C. ljungdahlii.
  • PETC medium component PETC medium NH 4 Cl 1 g KCl 0.1 g MgSO 4 •7H 2 O 0.2 g NaCl 0.8 g KH 2 PO 4 0.1 g CaCl 2 0.02 g
  • Trace metal solution see below
  • 10 ml Wolfe's vitamin solution see below
  • 10 ml Yeast extract optionally 1 g Resazurin (2 g/L stock) 0.5 ml NaHCO 3 2 g Reducing agent solution (see below) 0.006-0.008% (v/v) Fructose (for heterotrophic growth) 5 g
  • Amount per 1.0 L of trace Trace metal solution component metal solution Nitrilotriacetic acid 2 g MnSO 4 •H 2 O 1 g Fe(SO 4 ) 2 (NH 4 ) 2 •6H 2 O 0.8 g CoCl 2 •6H 2 O 0.2 g ZnSO 4 •7H 2 O 0.2 mg CuCl 2 •2H 2 O 0.02
  • This example demonstrates the construction of a strain comprising a p-hydroxybenzoate expression plasmid.
  • the nucleotide sequence for chorismate pyruvate lyase (SEQ ID NO: 1) was optimized (SEQ ID NO: 2) according to the C. autoethanogenum codon-usage table by GeneArt and cloned into the pMTL8315 expression vector ( FIG. 7 ) under control of the Wood-Ljungdahl pathway promoter (US 20110256600).
  • the coding sequence for a feedback-insensitive mutant 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase (aroG*) was also included, following ubiC in a bicistronic format ( FIG. 7 ).
  • the plasmid pARO_01 (SEQ ID NO: 9) was transformed into C. autoethanogenum LZ1561 (DSM23693) via conjugation with E. coli strain CA434 as donor.
  • Donor strains were grown overnight in LB media supplemented with 25 ⁇ g/mL chloramphenicol and 100 ⁇ g/mL spectinomycin. Cells from 1.5 mL of culture were harvested by centrifugation and washed in phosphate buffered saline (PBS). Inside an anaerobic workstation, the donor cell pellet was resuspended in 200 ⁇ L of exponentially growing recipient LZ1561. The conjugation mixture was spotted on PETC-MES agar medium and incubated at 37° C.
  • Liquid cultures were grown in 10 mL PETC-MES medium in serum bottles containing thiamphenicol and mill gas at 22 psi. Samples were taken daily to measure biomass ( FIG. 8 ) and pHBA ( FIG. 9 a and FIG. 9 b ).
  • LZ1561 (the control strain) has three technical replicates (i.e., grown and sampled three times). Two biological replicates of LZ1561 with pARO_01, were also prepared, each with three technical replicates. “Technical replicate” refers to growing and sampling each strain in separate experiments, while “biological replicate” refers to reproducing the strain from scratch. In this way, the biological replicates account for background biological variation in the microorganism, while technical replicates account for variation due to technical aspects including culture, sampling, and analysis methods.
  • FIG. 9 a shows that pHBA was produced repeatedly in separate instances.
  • FIG. 8 and FIG. 9 b give an overall representation of growth and pHBA productivity.
  • This example demonstrates the production of p-hydroxybenzoate via gas fermentation.
  • pHBA was validated by comparison to retention time and characteristic fragment ions of an authentic pHBA standard and predicted characteristic ions from the NIST mass spectrometry database ( FIG. 6 ).
  • pHBA production was observed in all cultures expressing the chorismate-pyruvate lyase encoded on the pMTL8315 expression vector.
  • the peak titre of pHBA observed in any one culture was 17 mg pHBA/L after eight days ( FIG. 9 b ). No pHBA was observed in the control sample without the expression vector.
  • Detectable levels of pHBA were produced by the genetically engineered bacterium and present in the culture.
  • This example demonstrates an experimental protocol for increasing the production of pHBA through enzyme engineering.
  • UbiC is subject to product inhibition through retention of pHBA.
  • the nucleic acid sequence encoding ubiC may be modified such that amino acids involved in product retention by the enzyme are mutated and release of product is enhanced. To do this, the amino acids involved in pHBA binding are identified by analysis of existing structures with bound product. Product inhibition is then minimised by mutating the amino acids involved in pHBA binding and retention.
  • a targeted library of ubiC mutants can be produced where different combinations of pHBA-binding amino acids are altered, and these mutant enzymes can be analysed with an enzyme assay. Improved mutants are then expressed in C. autoethanogenum LZ1561 to validate the strains with most improved pHBA productivity.
  • This example demonstrates the construction of a strain comprising a salicylate expression plasmid.
  • the nucleotide sequences for pchA (SEQ ID NO: 4) and pchB (SEQ ID NO: 6) were codon optimized and cloned into the expression vector under control of a tetracycline-inducible promoter.
  • the plasmid is transformed into C. autoethanogenum LZ1561 (DSM23693) via conjugation with E. coli strain CA434 as donor.
  • Donor strains were grown overnight in LB media supplemented with 25 ⁇ g/mL chloramphenicol and 100 ⁇ g/mL spectinomycin. Cells from 1.5 mL culture were harvested by centrifugation and washed in phosphate buffered saline (PBS).
  • PBS phosphate buffered saline
  • the donor cell pellet was resuspended in 200 ⁇ L of exponentially growing recipient C. autoethanogenum .
  • the conjugation mixture was spotted on PETC-MES agar medium and incubated at 37° C. After 24 hours the cells were scraped from the conjugation plate and spread on PETC-MES agar medium supplemented with 7.5 ⁇ g thiamphenicol/mL (Sigma) and 10 ⁇ g trimethoprim/mL (Sigma).
  • Three plasmid-bearing colonies (i.e. biological triplicates) isolates were grown in PETC-MES liquid medium containing 7.5 ⁇ g thiamphenicol/mL and with mill gas as the carbon source.
  • Liquid cultures were grown in 10 mL PETC-MES medium in serum bottles containing thiamphenicol and mill gas at 22 psi.
  • Biomass was monitored spectrophotometrically. At OD600 nm 0.3 expression of the salicylate biosynthetic pathway was induced by addition of 40 ng anhydrotetracycline/mL. Duplicate cultures (technical replicates of the three biological triplicates) were grown without the addition of anhydrotetracylcine such that the salicylate biosynthetic pathway remained uninduced. Samples were taken daily
  • Salicylate concentrations were measured using gas chromatography mass spectrometry analysis (GCMS), employing a Thermo Scientific ISQ LT GCMS equipped an Agilent CP-SIL 5CB-MS (50 m ⁇ 0.25 ⁇ m ⁇ 0.25 ⁇ m) column and autosampler. Samples were prepared by diluting 300 ⁇ L of sample with 600 ⁇ L of acetonitrile and 50 ⁇ L 0.1N NaOH. The samples were vortexed then centrifuged for 3 minutes at 14,000 rpm; 800 ⁇ L of the supernatant was transferred to a glass vial and the sample was dried in a Thermo SpeedVac®.
  • GCMS gas chromatography mass spectrometry analysis
  • the samples were then suspended in a solution of 100 ⁇ l of pyridine containing 22 mg/ml methoxyamine HCl then heated in a sealed glass vial for 60 minutes at 60° C. After which, 300 ⁇ L N,O-Bistrifluoroacetamide (BSTFA) was added then heated in a sealed glass vial for 60 minutes at 60° C. Samples were transferred to an autosampler for analysis using a 1.5 ⁇ L injection, a split ration of 20 to 1, and an inlet temperature of 250° C. Chromatography was performed with an oven program of 80° C. (no hold) to a ramp of 3° C./min to 140° C. to a ramp of 20° C./min to 230° C.
  • BSTFA N,O-Bistrifluoroacetamide
  • FIG. 11 a shows a comparison of biomass growth in the induced and un-induced samples.
  • FIG. 11 b shows that salicylate was produced repeatedly.
  • This example demonstrates knockout of pheA for enhanced production of chorismate-derived products.
  • pheA (e.g. from C. autoethanogenum , CAETHG_0905 (CP006763.1:973789 . . . 974925)) is a gene that encodes the enzyme prephenate synthase. Prephenate synthase catalyses the conversion of chorismate to prephenate, which is a precursor to the aromatic amino acids phenylalanine and tyrosine. pheA function was knocked out by disrupting the gene using the ClosTron method (Heap et al., J Microbiol Methods. 2010, 80(1):49-55). The ClosTron plasmid pMTL007C-E2 was generated by DNA2.0 and transformed into C.
  • autoethanogenum LZ1561 DSM23693 via conjugation with E. coli strain CA434 as donor.
  • Donor strains were grown overnight in LB media supplemented with 25 ⁇ g/mL chloramphenicol. Cells from 1.5 mL culture were harvested by centrifugation and washed in phosphate buffered saline (PBS). Inside an anaerobic workstation, the donor cell pellet was resuspended in 200 ⁇ L of exponentially growing recipient C. autoethanogenum LZ1561. The conjugation mixture was spotted on PETC agar media and incubated at 37° C.
  • PBS phosphate buffered saline
  • Plasmid-bearing isolates were grown in PETC-MES liquid medium containing 7.5 ⁇ g thiamphenicol/mL and with mill gas as the carbon source.
  • Colonies were streaked on PETC solid media containing the antibiotic clarithromycin (5 ⁇ g/mL). This step selected for integration of the intron retargeting sequence into the genome. Integration of the intron sequence into the target site results in an 1800 base pair insertion in the genome, which was screened for with colony PCR The PCR product of the positive ClosTron mutants were purified and sequenced to confirm the insertion site.
  • Liquid cultures were grown in 10 mL PETC-MES medium in serum bottles containing clarithromycin and mill gas at 22 psi. Glycerol stock was prepared from this serum bottle
  • Bioreactor experiments were carried out in a 2 L BioFlo 115 water jacket system (New Brunswick Scientific Corp., Edison, N.J.) with a working volume of 1.5 L.
  • the CSTR system was equipped with two six-bladed Rushton impellers and baffles enhance the mixing of fermentation broth and the gas to liquid mass transfer.
  • a pH and an oxidation-reduction potential (ORP) electrode (Broadley-James Corporation) were inserted through the headplate and their readings were recorded at 5 min intervals. pH was maintained at 5.0 by automated addition of a 5 M solution of ammonium hydroxide.
  • the inoculum was prepared from a glycerol stock.
  • One mL of glycerol stock was transferred into 50 mL of PETC media with 22 psi mill gas as carbon source.
  • the culture was incubated at 37° C. for on a shaker two to three days until a visible growth was observed.
  • the culture was then used to inoculate 200 mL of fresh media in 1 L-Schott bottle and mill gas was added to a pressure of 22 psi.
  • the Schott bottle was incubated for another 24 to 36 hours before being transferring to the fermenters.
  • the agitation was set at 200 rpm and the gas flow was set at 35 mL/min/L. After one day, the stirring rate was increased by 25 rpm at 4 hours intervals to the maximum value of 900 rpm. The gas flow was increased by 25 mL/min/L at 4 hours intervals to the maximum flow rate that the target CO uptake can be achieved.
  • the Na 2 S was added over the course of the fermentation with an initial pump rate of 0.3 mL/h and later increased in 0.2 mL/h increments when the H 2 S concentration in the headspace dropped below 200 ⁇ ppm.
  • the CO and H 2 consumption and CO 2 production along with the H 2 S concentration were measured hourly using gas chromatography (GC). Liquid samples were taken from the fermenter at regular intervals over the course of the fermentation to determine cell mass and metabolite concentrations using HPLC.
  • the fermenter After starting up in batch mode, the fermenter was turned to continuous when the OD reached a value of 2.
  • the media and nutrient inflow rates were controlled by one or more precision peristaltic pumps (Masterflex L/S digital drive pumps) while the fermenter volume was held constant by using a level probe that triggers a pump to remove fermentation broth from the CSTR.
  • the dilution rate was set in one step to 0.5 day ⁇ 1 and further increased to 1 day ⁇ 1 then to 1.7 day ⁇ 1 at 24 hour intervals.
  • An additional equipment was added to the fermentation was a hollow fibre membrane (GE Healthcare) with a pore size of 0.2 ⁇ m and a surface area of 1,200 cm 2 .
  • the membrane was used to increase the cell concentration in the fermentation.
  • the fermentation broth was pumped at high speed through the membrane and returned back to the fermenter while a stream of cell-free filtrate was pumped to the filtrate tank at a slower rate than the media pump rate. This allowed the retention time of the bacteria cell in the fermenter to increase.
  • the samples were then suspended in a solution of 400 ⁇ L of N,O-Bistrifluoroacetamide (BSTFA) and pyridine (3:1 ratio) and heated in a sealed glass vial for 60 minutes at 60° C.
  • Samples were transferred to an autosampler for analysis using a 1 ⁇ L injection, a split ration of 30 to 1, and an inlet temperature of 250° C.
  • Chromatography was performed with an oven program of 70° C. (no hold) to a ramp of 3° C./min to 110° C. to a ramp of 15° C./min to 230° C., followed by a final ramp of 40° C./min to 310° C. with a 3-min hold.
  • the column flow rate was 1.8 ml/min, with helium as the carrier gas.
  • the FID was kept at 320° C., with hydrogen at 40 ml/min, air at 400 ml/min, and helium at 20 ml/min as the makeup gas.
  • FIG. 12 shows the concentration of cis-4-hydroxycyclohexane carboxylic acid, 3,4-dihydroxybenzoic acid, and 2-aminobenzoic acid over the course of the fermentation run.
  • compound cis-4-hydroxycyclohexanecarboxylic acid increased to a concentration of about 0.9 g/L on day 6 of the fermentation.
  • 2-aminobenzoic acid accumulated to a concentration of about 0.45 g/L on day 8-9 of the fermentation.
  • 3,4-dihydroxybenzoic acid was produced in smaller amounts, peaking at a concentration of around 0.3 g/L between days 6-8.
  • a total accumulation of cis-4-hydroxycyclohexanecarboxylic acid, 2-aminobenzoic acid and 3,4-dihydroxybenzoic acid of >1.3 g/L was observed on day 6.
  • 2-Aminobenzoic acid is a known intermediate in the chorismate to tryptophan pathway. Anthranilate synthase catalyses the amination followed by the aromatization of chorismate to obtain the aromatic backbone of the tryptophan molecule. It is known that the gene expression of anthranilate synthase is highly regulated and subjected to feedback inhibition by the end product tryptophan (Dosselaere, Crit Rev Microbiol, 27: 75-131, 2001). 2-Aminobenzoic acid was only secreted into the fermentation broth when growth ceased indicating that it is an overflow product that was no longer reacted away when growth had stopped.

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